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SDC1 syndecan 1 [ Homo sapiens (human) ]

Gene ID: 6382, updated on 5-Mar-2024

Summary

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Official Symbol
SDC1provided by HGNC
Official Full Name
syndecan 1provided by HGNC
Primary source
HGNC:HGNC:10658
See related
Ensembl:ENSG00000115884 MIM:186355; AllianceGenome:HGNC:10658
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SDC; CD138; SYND1; syndecan
Summary
The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor types. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same protein. [provided by RefSeq, Jul 2008]
Expression
Broad expression in esophagus (RPKM 110.6), skin (RPKM 101.9) and 14 other tissues See more
Orthologs
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Genomic context

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See SDC1 in Genome Data Viewer
Location:
2p24.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (20200797..20225475, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (20234345..20259019, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (20400558..20425236, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 140, pseudogene Neighboring gene RNA, U6 small nuclear 961, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20387170-20387788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20396651-20397224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20400733-20401233 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20407001-20407625 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20407626-20408250 Neighboring gene uncharacterized LOC124905978 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:20408251-20408875 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20408876-20409501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20409502-20410126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15385 Neighboring gene Sharpr-MPRA regulatory region 13704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20414503-20415126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20415127-20415751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20422085-20422592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20422593-20423099 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20424859-20425538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20425539-20426218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20435326-20435884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20435885-20436443 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:20440896-20441042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11204 Neighboring gene DRG1 pseudogene 1 Neighboring gene RNA, U7 small nuclear 113 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. High expression of SDC1 in stromal cells is associated with good prognosis in colorectal cancer. Li Z, et al. Anticancer Drugs, 2023 Apr 1. PMID 36730554, Free PMC Article
  2. Syndecan 1 may slow the progression of subclinical atherosclerosis in patients with ankylosing spondylitis. Yilmaz PD, et al. Clin Exp Hypertens, 2023 Dec 31. PMID 36524421
  3. Expression of syndecan-1 in different grades of oral squamous cell carcinoma: An immunohistochemical study. Shetty PK, et al. J Cancer Res Ther, 2022 Dec. PMID 36510963
  4. Syndecan-1 in liver pathophysiology. Reszegi A, et al. Am J Physiol Cell Physiol, 2022 Aug 1. PMID 35704700
  5. The heparan sulphate proteoglycan Syndecan-1 (CD138) regulates tumour progression in a 3D model of ductal carcinoma in situ of the breast. D'Arcy C, et al. IUBMB Life, 2022 Oct. PMID 35587107

See all (421) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Soluble Endoglin and Syndecan-1 levels predicts the clinical outcome in COVID-19 patients.
    Title: Soluble Endoglin and Syndecan-1 levels predicts the clinical outcome in COVID-19 patients.
  2. CD9 co-operation with syndecan-1 is required for a major staphylococcal adhesion pathway.
    Title: CD9 co-operation with syndecan-1 is required for a major staphylococcal adhesion pathway.
  3. CLINICAL VALUE OF SYNDECAN-1 LEVELS IN TRAUMA BRAIN INJURY: A META-ANALYSIS.
    Title: CLINICAL VALUE OF SYNDECAN-1 LEVELS IN TRAUMA BRAIN INJURY: A META-ANALYSIS.
  4. Syndecan-1: A Novel Diagnostic and Therapeutic Target in Liver Diseases.
    Title: Syndecan-1: A Novel Diagnostic and Therapeutic Target in Liver Diseases.
  5. Neutrophil Extracellular Traps Are Induced by Coronavirus 2019 Disease-Positive Patient Plasma and Persist Longitudinally: A Possible Link to Endothelial Dysfunction as Measured by Syndecan-1.
    Title: Neutrophil Extracellular Traps Are Induced by Coronavirus 2019 Disease-Positive Patient Plasma and Persist Longitudinally: A Possible Link to Endothelial Dysfunction as Measured by Syndecan-1.
  6. SDC1 and ITGA2 as novel prognostic biomarkers for PDAC related to IPMN.
    Title: SDC1 and ITGA2 as novel prognostic biomarkers for PDAC related to IPMN.
  7. Binding of Trichinella spiralis C-type lectin with syndecan-1 on intestinal epithelial cells mediates larval invasion of intestinal epithelium.
    Title: Binding of Trichinella spiralis C-type lectin with syndecan-1 on intestinal epithelial cells mediates larval invasion of intestinal epithelium.
  8. Overexpression in metastatic breast cancer supports Syndecan-1 as a marker of invasiveness and poor prognosis.
    Title: Overexpression in metastatic breast cancer supports Syndecan-1 as a marker of invasiveness and poor prognosis.
  9. Dynamic interplay between sortilin and syndecan-1 contributes to prostate cancer progression.
    Title: Dynamic interplay between sortilin and syndecan-1 contributes to prostate cancer progression.
  10. The utility of syndecan-1 circulating levels as a biomarker in patients with previous or active COVID-19: a systematic review and meta-analysis.
    Title: The utility of syndecan-1 circulating levels as a biomarker in patients with previous or active COVID-19: a systematic review and meta-analysis.
Submit: New GeneRIF Correction See all GeneRIFs (357)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of syndecan 1 (SDC1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env The V3 region (amino acids 298-329) of HIV-1 gp120 contains the syndecan-binding site for HIV-1 via 6-O sulfated motifs; a single conserved arginine (Arg-298) in the V3 region of gp120 governs HIV-1 binding to syndecans PubMed
Tat tat HIV-1 Tat tethered to the surface of syndecan-1 expression B-lymphoid cells or of peripheral blood monocytes promotes their transendothelial migration in vitro in response to CXCL12 or CCL5, respectively PubMed
tat Binding of HIV-1 Tat to heparan sulfate proteoglycans is competed out by the heparin-binding factor bFGF PubMed
tat Cell membrane heparin sulfate proteoglycans bind to the basic region of HIV-1 Tat (amino acids 49-57) and act as receptors for extracellular Tat uptake, an effect that may contribute to the angiogenic properties of Tat in promoting Kaposi's sarcoma PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cargo receptor activity IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Sertoli cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in myoblast development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of exosomal secretion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of extracellular exosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in receptor-mediated endocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in response to cAMP IEA
Inferred from Electronic Annotation
more info
  
involved_in response to calcium ion IEA
Inferred from Electronic Annotation
more info
  
involved_in response to glucocorticoid IEA
Inferred from Electronic Annotation
more info
  
involved_in response to hydrogen peroxide IEA
Inferred from Electronic Annotation
more info
  
involved_in response to toxic substance IEA
Inferred from Electronic Annotation
more info
  
involved_in striated muscle cell development IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in ureteric bud development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi lumen TAS
Traceable Author Statement
more info
  
is_active_in cell surface IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cell surface IDA
Inferred from Direct Assay
more info
 PubMed 
located_in external side of plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular exosome HDA PubMed 
located_in lysosomal lumen TAS
Traceable Author Statement
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
part_of protein-containing complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
syndecan-1
Names
CD138 antigen
heparan sulfate proteoglycan fibroblast growth factor receptor
syndecan proteoglycan 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_050639.2 RefSeqGene

    Range
    5345..29678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001006946.2 → NP_001006947.2  syndecan-1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC104792
    Consensus CDS
    CCDS1697.1
    UniProtKB/Swiss-Prot
    D6W523, P18827, Q53QV0, Q546D3, Q96HB7
    Related
    ENSP00000370542.1, ENST00000381150.5
    Conserved Domains (1) summary
    pfam01034
    Location:245 → 308
    Syndecan; Syndecan domain

  2. NM_002997.5 → NP_002988.4  syndecan-1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC104792
    Consensus CDS
    CCDS1697.1
    UniProtKB/Swiss-Prot
    D6W523, P18827, Q53QV0, Q546D3, Q96HB7
    Related
    ENSP00000254351.4, ENST00000254351.9
    Conserved Domains (1) summary
    pfam01034
    Location:245 → 308
    Syndecan; Syndecan domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    20200797..20225475 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005262622.3 → XP_005262679.1  syndecan-1 isoform X3

    Conserved Domains (1) summary
    pfam01034
    Location:227 → 290
    Syndecan; Syndecan domain

  2. XM_005262620.5 → XP_005262677.1  syndecan-1 isoform X1

    Conserved Domains (1) summary
    pfam01034
    Location:269 → 332
    Syndecan; Syndecan domain

  3. XM_005262621.3 → XP_005262678.3  syndecan-1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    20234345..20259019 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343337.1 → XP_054199312.1  syndecan-1 isoform X3

  2. XM_054343335.1 → XP_054199310.1  syndecan-1 isoform X1

  3. XM_054343336.1 → XP_054199311.1  syndecan-1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P18827.3 GenPept UniProtKB/Swiss-Prot:P18827

Gene LinkOut

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